(083d7a0b) · Commits · 郑智淋 / lammps

src/XTC/dump_xtc.cpp

+0 −3

Original line number	Diff line number	Diff line
		@@ -225,12 +225,10 @@ void DumpXTC::pack(int *ids)
		int iz = (image[i] >> 20) - 512;

		if (domain->triclinic) {
		buf[m++] = tag[i];
		buf[m++] = sfactor * (x[i][0] + ix * xprd + iy * xy + iz * xz);
		buf[m++] = sfactor * (x[i][1] + iy * yprd + iz * yz);
		buf[m++] = sfactor * (x[i][2] + iz * zprd);
		} else {
		buf[m++] = tag[i];
		buf[m++] = sfactor * (x[i][0] + ix * xprd);
		buf[m++] = sfactor * (x[i][1] + iy * yprd);
		buf[m++] = sfactor * (x[i][2] + iz * zprd);
		@@ -241,7 +239,6 @@ void DumpXTC::pack(int *ids)
		} else {
		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {
		buf[m++] = tag[i];
		buf[m++] = sfactor*x[i][0];
		buf[m++] = sfactor*x[i][1];
		buf[m++] = sfactor*x[i][2];

src/dump.cpp

+23 −14

Original line number	Diff line number	Diff line
		@@ -70,7 +70,7 @@ Dump::Dump(LAMMPS lmp, int narg, char *arg) : Pointers(lmp)

		maxbuf = maxsort = maxproc = 0;
		buf = bufsort = NULL;
		idsort = index = proclist = NULL;
		ids = idsort = index = proclist = NULL;
		irregular = NULL;

		// parse filename for special syntax
		@@ -123,6 +123,7 @@ Dump::~Dump()

		memory->sfree(buf);
		memory->sfree(bufsort);
		memory->sfree(ids);
		memory->sfree(idsort);
		memory->sfree(index);
		memory->sfree(proclist);
		@@ -148,16 +149,16 @@ void Dump::init()
		init_style();

		if (!sort_flag) {
		memory->sfree(buf);
		memory->sfree(bufsort);
		memory->sfree(ids);
		memory->sfree(idsort);
		memory->sfree(index);
		memory->sfree(proclist);
		delete irregular;

		maxbuf = maxsort = maxproc = 0;
		buf = bufsort = NULL;
		idsort = index = proclist = NULL;
		maxsort = maxproc = 0;
		bufsort = NULL;
		ids = idsort = index = proclist = NULL;
		irregular = NULL;
		}

		@@ -252,7 +253,7 @@ void Dump::write()
		if (me == 0) {
		for (int iproc = 0; iproc < nprocs; iproc++) {
		if (iproc) {
		MPI_Irecv(buf,maxbuf,MPI_DOUBLE,iproc,0,world,&request);
		MPI_Irecv(buf,maxbuf*size_one,MPI_DOUBLE,iproc,0,world,&request);
		MPI_Send(&tmp,0,MPI_INT,iproc,0,world);
		MPI_Wait(&request,&status);
		MPI_Get_count(&status,MPI_DOUBLE,&nlines);
		@@ -455,11 +456,19 @@ void Dump::sort()

		// copy data from bufsort to buf using index

		if (nme > maxbuf) {
		maxbuf = nme;
		int nmax;
		if (multiproc) nmax = nme;
		else MPI_Allreduce(&nme,&nmax,1,MPI_INT,MPI_MAX,world);

		if (nmax > maxbuf) {
		maxbuf = nmax;
		memory->sfree(buf);
		buf = (double *)
		memory->smalloc(maxbufsize_onesizeof(double),"dump:buf");
		if (sortcol == 0) {
		memory->sfree(ids);
		ids = (int ) memory->smalloc(maxbufsizeof(int),"dump:ids");
		}
		}

		int nbytes = size_one*sizeof(double);
		@@ -468,9 +477,9 @@ void Dump::sort()
		}

		/* ----------------------------------------------------------------------
		compare two atom IDs in sort data structure
		called via qsort_r in sort() method
		is a static method so access sort data structure via ptr
		compare two atom IDs
		called via qsort() in sort() method
		is a static method so access data via dumpptr
		------------------------------------------------------------------------- */

		int Dump::idcompare(const void pi, const void pj)
		@@ -486,9 +495,9 @@ int Dump::idcompare(const void pi, const void pj)
		}

		/* ----------------------------------------------------------------------
		compare two buffer quantities in sort data structure with size_one stride
		called via qsort_r in sort() method
		is a static method so access sort data structure via ptr
		compare two buffer values with size_one stride
		called via qsort() in sort() method
		is a static method so access data via dumpptr
		------------------------------------------------------------------------- */

		int Dump::bufcompare(const void pi, const void pj)

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